Base class for moves that can obey detailed balance. More...

#include <ThermodynamicMover.hh>

Inheritance diagram for protocols::canonical_sampling::ThermodynamicMover:

Public Member Functions
	ThermodynamicMover ()
	Default constructor. More...

	~ThermodynamicMover () override
	Default destructor. More...

virtual void	initialize_simulation (core::pose::Pose &pose, protocols::canonical_sampling::MetropolisHastingsMover const &metropolis_hastings_mover, core::Size cycle)
	Callback executed before any Monte Carlo trials are attempted. More...

virtual void	observe_after_metropolis (protocols::canonical_sampling::MetropolisHastingsMover const &metropolis_hastings_mover)
	Callback executed after the Metropolis criterion is evaluated. More...

core::Real	last_proposal_density_ratio () override
	Return the proposal density ratio for last apply method. More...

virtual void	finalize_simulation (core::pose::Pose &pose, protocols::canonical_sampling::MetropolisHastingsMover const &metropolis_hastings_mover)
	Callback executed after all Monte Carlo trials are completed. More...

virtual bool	preserve_detailed_balance () const =0
	Return true if detailed balance is being preserved (i.e. no branch angle optimization). More...

virtual void	set_preserve_detailed_balance (bool preserve_detailed_balance)=0
	Set to true if detailed balance should be preserved (i.e. no branch angle optimization). This will be set to true for all movers used by MetropolisHastingsMover. More...

virtual bool	is_multi_trial ()
	Return true if the move performs multiple trials on each apply. More...

virtual core::Real	last_inner_score_delta_over_temperature ()
	If this is a multi-trial move, return the change in internal score/temperature caused by the last call to apply(). More...

virtual protocols::canonical_sampling::MetropolisHastingsMoverAP	metropolis_hastings_mover ()
	If this is a multi-trial move, return the MetropolisHastingsMover being used internally. More...

virtual void	set_metropolis_hastings_mover (protocols::canonical_sampling::MetropolisHastingsMoverAP metropolis_hastings_mover)
	If this is a multi-trial move, set the MetropolisHastingsMover to be used internally. More...

virtual utility::vector1 < core::id::TorsionID_Range >	torsion_id_ranges (core::pose::Pose &pose)=0
	Return a list specifying which torsions may be perturbed by apply(), and the in what range each perturbation may be. More...

virtual utility::vector1 < core::id::DOF_ID_Range >	dof_id_ranges (core::pose::Pose &pose)
	Return a list specifying which degrees of freedom may be perturbed by apply(), and the in what range each perturbation may be. More...

Public Member Functions inherited from protocols::moves::Mover
	Mover ()

virtual MoverOP	create ()

MoverCOP	get_self_ptr () const

MoverOP	get_self_ptr ()

MoverCAP	get_self_weak_ptr () const

MoverAP	get_self_weak_ptr ()

	Mover (std::string const &type_name)
	sets the type for a mover; name_ has been removed (2010/05/14) More...

virtual void	apply (Pose &)=0
	Main Method. More...

virtual void	test_move (Pose &pose)
	: Unit test support function. Apply one move to a given pose. Allows extra test specific functions to be called before applying More...

virtual MoverOP	clone () const
	Return a clone of the Mover object. More...

virtual bool	reinitialize_for_each_job () const
	Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on each use. More...

virtual bool	reinitialize_for_new_input () const
	Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose). More...

virtual MoverOP	fresh_instance () const
	Generates a new Mover object freshly created with the default ctor. More...

MoverStatus	get_last_move_status () const
	end parser interface, start Job Distributor interface///////////// More...

void	reset_status ()
	resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s. More...

virtual core::pose::PoseOP	get_additional_output ()
	Mechanism by which a mover may return multiple output poses from a single input pose. More...

void	set_type (std::string const &setting)
	Set the 'type' string. More...

std::string	get_type () const

void	type (const std::string &type_in)
	Set the 'type' string. More...

std::string const &	type () const
	Get the set 'type' string. More...

virtual void	set_input_pose (PoseCOP pose)
	setter for poses contained for rms More...

virtual void	set_native_pose (PoseCOP pose)
	setter for native poses contained for rms -— we should get rid of this method? it is widely used, but a bit unsafe More...

PoseCOP	get_input_pose () const

PoseCOP	get_native_pose () const

virtual void	parse_my_tag (TagCOP tag, basic::datacache::DataMap &data)
	Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...

virtual std::string	get_name () const =0
	Each derived class must specify its name. The class name. More...

void	set_current_job (protocols::jobdist::BasicJobCOP job)

jobdist::BasicJobCOP	get_current_job () const

virtual void	set_current_tag (std::string const &new_tag)

std::string	get_current_tag () const
	A tag is a unique identifier used to identify structures produced by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor. More...

virtual void	show (std::ostream &output=std::cout) const
	Outputs details about the Mover, including current settings. More...

virtual void	clear_info ()
	Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file. More...

virtual Strings &	info ()
	non-const accessor More...

virtual Strings const &	info () const
	const accessor More...

virtual void	provide_citation_info (basic::citation_manager::CitationCollectionList &) const
	Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. More...

Additional Inherited Members
Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagCOP	TagCOP

typedef core::pose::Pose	Pose

typedef core::pose::PoseCOP	PoseCOP

typedef std::list< std::string >	Strings

Static Public Member Functions inherited from protocols::moves::Mover
static std::string	name ()

static void	register_options ()
	Overload this static method if you access options within the mover. More...

Protected Member Functions inherited from protocols::moves::Mover
void	set_last_move_status (MoverStatus status)
	nonvirtual setter for MoverStatus last_status_. Protected means that only the mover itself will be able to change its own status. The job distributor (august 08 vintage) is aware of status set with this function and will do what the MoverStatus says. More...

Detailed Description

Base class for moves that can obey detailed balance.

In order to sample a thermodynamic state using a Monte Carlo simulation, the moves must obey detailed balance. This base class provides a framework for writing moves that can obey this condition. One interesting method is set_preserve_detailed_balance(), which indicates whether or not detailed balance needs to be obeyed. This flag makes it possible to implement fancy (but biased) features for use in contexts where rigorous thermodynamic sampling isn't needed. If the move requires a non-unity proposal ratio to obey detailed balance, it can reimplement last_proposal_density_ratio(). Support for movers that make multiple trial moves under the hood is provided by is_multi_trial() and its related methods. A number of callbacks, including initialize_simulation(), observe_after_metropolis(), and finalize_simulation(), are also defined to let the mover react to certain milestones in the simulation.

Constructor & Destructor Documentation

protocols::canonical_sampling::ThermodynamicMover::ThermodynamicMover ( )

Default constructor.

protocols::canonical_sampling::ThermodynamicMover::~ThermodynamicMover ( )

overridedefault

Default destructor.

Member Function Documentation

utility::vector1< core::id::DOF_ID_Range > protocols::canonical_sampling::ThermodynamicMover::dof_id_ranges ( core::pose::Pose & pose )

virtual

Return a list specifying which degrees of freedom may be perturbed by apply(), and the in what range each perturbation may be.

Torsion DOFs that would be returned by torsion_id_ranges() are not returned by this function too.

Reimplemented in protocols::simple_moves::ShearMover, protocols::backrub::BackrubMover, protocols::simple_moves::SmallMover, protocols::simple_moves::BackboneMover, protocols::simple_moves::sidechain_moves::SidechainMover, and protocols::simple_moves::sidechain_moves::SidechainMoverBase.

void protocols::canonical_sampling::ThermodynamicMover::finalize_simulation	(	core::pose::Pose &	pose,
		protocols::canonical_sampling::MetropolisHastingsMover const &	metropolis_hastings_mover
	)

virtual

Callback executed after all Monte Carlo trials are completed.

Reimplemented in protocols::backrub::BackrubSidechainMover.

void protocols::canonical_sampling::ThermodynamicMover::initialize_simulation	(	core::pose::Pose &	pose,
		protocols::canonical_sampling::MetropolisHastingsMover const &	metropolis_hastings_mover,
		core::Size	cycle
	)

virtual

Callback executed before any Monte Carlo trials are attempted.

Reimplemented in protocols::simple_moves::sidechain_moves::SidechainMCMover, protocols::backrub::BackrubMover, protocols::backrub::BackrubSidechainMover, protocols::simple_moves::sidechain_moves::SidechainMover, and protocols::simple_moves::sidechain_moves::SidechainMoverBase.

bool protocols::canonical_sampling::ThermodynamicMover::is_multi_trial ( )

virtual

Return true if the move performs multiple trials on each apply.

See also: last_inner_score_delta_over_temperature(); metropolis_hastings_mover(); set_metropolis_hastings_mover()

Reimplemented in protocols::simple_moves::sidechain_moves::SidechainMCMover.

core::Real protocols::canonical_sampling::ThermodynamicMover::last_inner_score_delta_over_temperature ( )

virtual

If this is a multi-trial move, return the change in internal score/temperature caused by the last call to apply().

See also: is_multi_trial()

Reimplemented in protocols::simple_moves::sidechain_moves::SidechainMCMover.

core::Real protocols::canonical_sampling::ThermodynamicMover::last_proposal_density_ratio ( )

overridevirtual

Return the proposal density ratio for last apply method.

Reimplemented from protocols::moves::Mover.

Reimplemented in protocols::simple_moves::sidechain_moves::SidechainMover, protocols::simple_moves::sidechain_moves::SidechainMoverBase, protocols::simple_moves::sidechain_moves::SidechainMCMover, protocols::simple_moves::BBGaussianMover, and protocols::kinematic_closure::BalancedKicMover.

protocols::canonical_sampling::MetropolisHastingsMoverAP protocols::canonical_sampling::ThermodynamicMover::metropolis_hastings_mover ( )

virtual

If this is a multi-trial move, return the MetropolisHastingsMover being used internally.

See also: is_multi_trial()

Reimplemented in protocols::simple_moves::sidechain_moves::SidechainMCMover.

void protocols::canonical_sampling::ThermodynamicMover::observe_after_metropolis ( protocols::canonical_sampling::MetropolisHastingsMover const & metropolis_hastings_mover )

virtual

Callback executed after the Metropolis criterion is evaluated.

Reimplemented in protocols::backrub::BackrubSidechainMover.

virtual bool protocols::canonical_sampling::ThermodynamicMover::preserve_detailed_balance ( ) const

pure virtual

Return true if detailed balance is being preserved (i.e. no branch angle optimization).

Implemented in protocols::backrub::BackrubMover, protocols::simple_moves::BackboneMover, protocols::backrub::BackrubSidechainMover, protocols::simple_moves::sidechain_moves::SidechainMover, protocols::simple_moves::sidechain_moves::SidechainMoverBase, protocols::simple_moves::BBGaussianMover, protocols::rigid::RigidBodyMover, protocols::kinematic_closure::BalancedKicMover, and protocols::rigid::UniformRigidBodyMover.

void protocols::canonical_sampling::ThermodynamicMover::set_metropolis_hastings_mover ( protocols::canonical_sampling::MetropolisHastingsMoverAP metropolis_hastings_mover )

virtual

If this is a multi-trial move, set the MetropolisHastingsMover to be used internally.

See also: is_multi_trial()

Reimplemented in protocols::simple_moves::sidechain_moves::SidechainMCMover.

virtual void protocols::canonical_sampling::ThermodynamicMover::set_preserve_detailed_balance ( bool preserve_detailed_balance )

pure virtual

Set to true if detailed balance should be preserved (i.e. no branch angle optimization). This will be set to true for all movers used by MetropolisHastingsMover.

Implemented in protocols::backrub::BackrubMover, protocols::simple_moves::BackboneMover, protocols::backrub::BackrubSidechainMover, protocols::simple_moves::sidechain_moves::SidechainMover, protocols::simple_moves::sidechain_moves::SidechainMoverBase, protocols::simple_moves::BBGaussianMover, protocols::rigid::RigidBodyMover, protocols::kinematic_closure::BalancedKicMover, and protocols::rigid::UniformRigidBodyMover.

virtual utility::vector1<core::id::TorsionID_Range> protocols::canonical_sampling::ThermodynamicMover::torsion_id_ranges ( core::pose::Pose & pose )

pure virtual

Return a list specifying which torsions may be perturbed by apply(), and the in what range each perturbation may be.

This method should probably not be pure virtual, and in fact should probably not even exist. I searched most of the codebase, and could only find it being used in one pilot app. It is also a somewhat difficult method to write, which means that most of the implementations are either untested or no-ops. It might be better to remove the method altogether and implement it on a class-by-class basis as necessary.

Implemented in protocols::simple_moves::ShearMover, protocols::backrub::BackrubMover, protocols::simple_moves::SmallMover, protocols::backrub::BackrubSidechainMover, protocols::simple_moves::sidechain_moves::SidechainMover, protocols::simple_moves::sidechain_moves::SidechainMoverBase, protocols::simple_moves::BBGaussianMover, protocols::rigid::RigidBodyMover, protocols::kinematic_closure::BalancedKicMover, and protocols::rigid::UniformRigidBodyMover.

The documentation for this class was generated from the following files:

src/protocols/canonical_sampling/ThermodynamicMover.hh
src/protocols/canonical_sampling/ThermodynamicMover.cc

Public Member Functions

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation